GEO series
Persistent cortical excitatory neuron dysregulation in adult Chd8 haploinsufficient mice
GSE300997
Mus musculus (mouse)
Single-nucleus RNA-seq
127 samples
Submitted 2026/01/01
Platform GPL24247Platform GPL34475
At a glance
Single-nucleus RNA-seq · mouse · 127 samples
- What it is
- Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Mus musculus (mouse)
- Samples
- 127 samples: 31 conditions, mostly in duplicateGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Persistent cortical excitatory neuron dysregulation in adult Chd8 haploinsufficient micebioRxiv : the preprint server for biology · 2025
Summary (written by the submitters)
CHD8 mutations cause autism spectrum disorder, cognitive deficits, and macrocephaly. Chd8+/- mouse models exhibit macrocephaly and transcriptional pathology, with inconsistent findings regarding neurogenesis, neuron function, and behavior. Via stereology and single nuclei transcriptomics (snRNA-seq), we found increased Chd8+/- cortical volume was not explained by increase in neuron number.
Read the full summary ↓
Differential expression (DE) was present across cortical cell types, with excitatory neurons exhibiting high DE burden and shared and subclass-specific DE signatures. Bulk RNA-seq DE of constitutive Chd8+/- and conditional Camk2a-Cre Chd8+/- mice identified shared transcriptional pathology. DE in synaptosomal versus nuclear mRNA identified overlapping DEGs, but also significant differences and exaggerated synaptosomal changes. Building on DE findings implicating glutamatergic neurons, we found Chd8+/- mice exhibited altered excitatory neuron spine density and dynamics, decreased GCaMP activity correlation, and sleep perturbation. Thus, Chd8 haploinsufficiency causes lasting excitatory neuron dysfunction, perturbs RNA regulation beyond transcription, and impacts neuronal properties, cortical microcircuits, and behavior.
Published in
Canales CP, Lozano SA, Frost NA et al.
· bioRxiv : the preprint server for biology 2025
· PMID 40501938
· doi:10.1101/2025.06.04.657776
This dataset
Download · which file do I need?
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
1 · Just have a look
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
2 · Re-analyse it
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE300997_RAW.tar (it can run to tens of gigabytes).
3 · Start from the raw reads
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1282974 and SRA study SRP595582. Searching any of these in the dataset finder brings you back here.
Study design
31 conditions, mostly in duplicate
Cortex, whole cell, female Chd8+/– germline H… ×9
Cortex, whole cell, male WT, biol ×8
Cortex, whole cell, female WT, biol ×7
Cortex, whole cell, male Chd8+/– germline HET… ×7
Cortex, whole cell nuclear fraction, male WT,… ×7
Cortex, whole cell synaptic fraction, male WT… ×6
Cortex, cytosolic fraction, female Chd8+/– ge… ×6
Cortex, whole cell, male Chd8^+/flox, biol ×5
+25 more
Supports a between-group comparison across 125 samples.
How we read this: 31 replicated groups read from 127 sample titles; they account for 125 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
Samples in this study
- GSM9073375 Cortex, whole cell, female Chd8+/– germline HET, biol rep 1 Cortex, whole cell, fem…
- GSM9073376 Cortex, whole cell, female Chd8+/– germline HET, biol rep 2 Cortex, whole cell, fem…
- GSM9073377 Cortex, whole cell, male WT, biol rep 1 Cortex, whole cell, mal…
- GSM9073378 Cortex, whole cell, female WT, biol rep 1 Cortex, whole cell, fem…
- GSM9073379 Cortex, whole cell, female WT, biol rep 2 Cortex, whole cell, fem…
- GSM9073380 Cortex, whole cell, male WT, biol rep 2 Cortex, whole cell, mal…
- GSM9073381 Cortex, whole cell, female Chd8+/– germline HET, biol rep 3 Cortex, whole cell, fem…
- GSM9073382 Cortex, whole cell, male Chd8+/– germline HET, biol rep 1 Cortex, whole cell, mal…
- GSM9073383 Cortex, whole cell, female Chd8+/– germline HET, biol rep 4 Cortex, whole cell, fem…
- GSM9073384 Cortex, whole cell, female WT, biol rep 3 Cortex, whole cell, fem…
- GSM9073385 Cortex, whole cell, male Chd8+/– germline HET, biol rep 2 Cortex, whole cell, mal…
- GSM9073386 Cortex, whole cell, male Chd8+/– germline HET, biol rep 3 Cortex, whole cell, mal…
- GSM9073387 Cortex, whole cell, female WT, biol rep 4 Cortex, whole cell, fem…
- GSM9073388 Cortex, whole cell, male WT, biol rep 3 Cortex, whole cell, mal…
- GSM9073389 Cortex, whole cell, male Chd8+/– germline HET, biol rep 4 Cortex, whole cell, mal…
- GSM9073390 Cortex, whole cell, male WT, biol rep 4 Cortex, whole cell, mal…
- GSM9073391 Cortex, whole cell, female Chd8+/– germline HET, biol rep 5 Cortex, whole cell, fem…
- GSM9073392 Cortex, whole cell, female Chd8+/– germline HET, biol rep 6 Cortex, whole cell, fem…
- GSM9073393 Cortex, whole cell, female WT, biol rep 5 Cortex, whole cell, fem…
- GSM9073394 Cortex, whole cell, male Chd8+/– germline HET, biol rep 5 Cortex, whole cell, mal…
- GSM9073395 Cortex, whole cell, male WT, biol rep 5 Cortex, whole cell, mal…
- GSM9073396 Cortex, whole cell, female Chd8+/– germline HET, biol rep 7 Cortex, whole cell, fem…
- GSM9073397 Cortex, whole cell, male WT, biol rep 6 Cortex, whole cell, mal…
- GSM9073398 Cortex, whole cell, male Chd8+/– germline HET, biol rep 6 Cortex, whole cell, mal…
- GSM9073399 Cortex, whole cell, female WT, biol rep 6 Cortex, whole cell, fem…
- GSM9073400 Cortex, whole cell, female Chd8+/– germline HET, biol rep 8 Cortex, whole cell, fem…
- GSM9073401 Cortex, whole cell, female WT, biol rep 7 Cortex, whole cell, fem…
- GSM9073402 Cortex, whole cell, male WT, biol rep 7 Cortex, whole cell, mal…
- GSM9073403 Cortex, whole cell, male WT, biol rep 8 Cortex, whole cell, mal…
- GSM9073404 Cortex, whole cell, male Chd8+/– germline HET, biol rep 7 Cortex, whole cell, mal…
- GSM9073405 Cortex, whole cell, female Chd8+/– germline HET, biol rep 9 Cortex, whole cell, fem…
- GSM9073406 Cortex, whole cell, female Chd8^+/flox, biol rep 1 Cortex, whole cell, fem…
- GSM9073407 Cortex, whole cell, male Chd8^+/flox, biol rep 1 Cortex, whole cell, mal…
- GSM9073408 Cortex, whole cell, male, Camk2a-CRE Chd8+/flox, biol rep 1 Cortex, whole cell, mal…
- GSM9073409 Cortex, whole cell, male Chd8^+/flox, biol rep 2 Cortex, whole cell, mal…
- GSM9073410 Cortex, whole cell, male Chd8^+/flox, biol rep 3 Cortex, whole cell, mal…
- GSM9073411 Cortex, whole cell, male, Camk2a-CRE Chd8+/flox, biol rep 2 Cortex, whole cell, mal…
- GSM9073412 Cortex, whole cell, male, Camk2a-CRE Chd8+/flox, biol rep 3 Cortex, whole cell, mal…
- GSM9073413 Cortex, whole cell, female Chd8^+/flox, biol rep 2 Cortex, whole cell, fem…
- GSM9073414 Cortex, whole cell, female Chd8^+/flox, biol rep 3 Cortex, whole cell, fem…
+ 87 more — browse all 127 samples with per-sample file links →
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Share this dataset
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.